I had updated to R# 6.1 a few weeks ago and that didn't seem to cause any issues with StyleCop 4.6. I didn't lose my settings until I upgraded StyleCop from 4.6 to 4.7.

I should clarify that I am not talking about R# settings for the Stylecop settings as they show up in R#. I am talking specifically about the Settings.StyleCop settings file and opening this file from the StyleCopSettingsEditor app.